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Figure 3 | BMC Evolutionary Biology

Figure 3

From: Visualization and Exploration of Conserved Regulatory Modules Using ReXSpecies 2

Figure 3

CR3 pattern at UCSC. The pattern found in the murine CR3 region at the UCSC genome browser. The pattern is shown as one track, more patterns would be in a new track. The tracks are sorted by branch length score [37], which is shown in the track description. The color and the number in the track description are unique for each pattern, the ancestral species predicted to be the origins of the pattern are also given in the track description. (If all transcription factor binding sites of a pattern are predicted for mouse, this is denoted using an exclamation mark.) If a pattern does not occur for mouse at all, it is not shown in the UCSC figure. The color intensity of the glyphs (squares/rectangles) that represent the binding sites reflects the matrix similarity score. This score is based on the position specific scoring matrix match that yielded the murine transcription factor binding site prediction. Below the prediction tracks, the wiki track is shown. This track contains annotations that we have listed in [5], see also Table 1. The wiki track entries are linked with the PubMed [42] entries of the papers that published the corresponding transcription factor binding site. At the bottom of the figure, sequence conservation is shown. We analyzed the PhastCons [43] most conserved elements only; also we did not analyze the untranslated regions (UTRs) of genes. The very first track lists the nucleotide bases; stop codons (*) in the "amino acid track" indicate that the region is non-coding.

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